New Version
Fixed default value for -d/--pe-delimiter
Typo
Version
Fixed "Unable to open output file" error when building the reference
index (calling NextGenMap only with -r option)
Clean up
Added parameter -Q/--min-mq
version
Write tags from input sam to output sam
Close file after determining correct parser
parameter --keep-tags added
When specified NextGenMap copies BAM/SAM tags from the input file to the
output file.
Changed error handling for file parsers
Mason: batch size fix (CPU)
Fixed: Wrong strand information (ZS flag) for single end BS data
Typo
Fixed: Paired end bug: -1 -2

Names of mates are now checked. Can be skipped using --skip-mate-check
Debug code removed
Score Writer added. Not used yet.
Fixed: Header Problem with Picard (181)

+BAM output for paired end data fixed.
Fixed: Tried to access invalid reference sequence (2147483646 7ffffffe)
on E. Coli (#177)

Moved location convert to SequenceProvider
Fixed: Segfault reference building (#173)